NAME

       fastq_masker - Masks nucleotides with 'N' (or other character) based on quality

DESCRIPTION

       usage:  fastq_masker  [-h]  [-v] [-q N] [-r C] [-z] [-i INFILE] [-o OUTFILE] Part of FASTX
       Toolkit 0.0.14 by A. Gordon (assafgordon@gmail.com)

       [-h]   = This helpful help screen.

       [-q N] = Quality threshold - nucleotides with lower quality will be masked

              Default is 10.

       [-r C] = Replace low-quality nucleotides with character C. Default is 'N'

       [-z]   = Compress output with GZIP.

       [-i INFILE]
              = FASTQ input file. default is STDIN.

              [-o OUTFILE] = FASTQ output file. default is  STDOUT.   [-v]          =  Verbose  -
              report number of sequences.

       If [-o] is specified,
              report will be printed to STDOUT.

              If  [-o]  is  not  specified (and output goes to STDOUT), report will be printed to
              STDERR.

SEE ALSO

       The quality of  this  automatically  generated  manpage  might  be  insufficient.   It  is
       suggested to visit

              http://hannonlab.cshl.edu/fastx_toolkit/commandline.html

       to get a better layout as well as an overview about connected FASTX tools.